Study protocol: Comparison of different risk prediction modelling approaches for COVID-19 related death using the OpenSAFELY platform

Wellcome Open Research, vol. 5, pp. 243

Abstract

On March 11th 2020, the World Health Organization characterised COVID-19 as a pandemic. Responses to containing the spread of the virus have relied heavily on policies involving restricting contact between people. Evolving policies regarding shielding and individual choices about restricting social contact will rely heavily on perceived risk of poor outcomes from COVID-19. In order to make informed decisions, both individual and collective, good predictive models are required. For outcomes related to an infectious disease, the performance of any risk prediction model will depend heavily on the underlying prevalence of infection in the population of interest. Incorporating measures of how this changes over time may result in important improvements in prediction model performance. This protocol reports details of a planned study to explore the extent to which incorporating time-varying measures of infection burden over time improves the quality of risk prediction models for COVID-19 death in a large population of adult patients in England. To achieve this aim, we will compare the performance of different modelling approaches to risk prediction, including static cohort approaches typically used in chronic disease settings and landmarking approaches incorporating time-varying measures of infection prevalence and policy change, using COVID-19 related deaths data linked to longitudinal primary care electronic health records data within the OpenSAFELY secure analytics platform.

Authors 42

1. Elizabeth Williamson

   London School of Hygiene & Tropical Medicine

   Affiliation as printed

   London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK

2. John Tazare

   London School of Hygiene & Tropical Medicine

   Affiliation as printed

   London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK

3. Krishnan Bhaskaran

   University of Oxford

   Affiliation as printed

   The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX26GG, UK

4. Alex J Walker

   National Institute for Health and Care Research · London School of Hygiene & Tropical Medicine

   Affiliation as printed

   London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK

   NIHR Health Protection Research Unit (HPRU) in Immunisation, London, UK

5. Helen I McDonald

   London School of Hygiene & Tropical Medicine

   Affiliation as printed

   London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK

6. Laurie A. Tomlinson

   University of Oxford

   Affiliation as printed

   The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX26GG, UK

7. Seb Bacon
   Affiliation as printed

   TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, UK

8. Chris J Bates

   University of Oxford

   Affiliation as printed

   The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX26GG, UK

9. Helen J Curtis

   London School of Hygiene & Tropical Medicine

   Affiliation as printed

   London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK

10. Harriet J. Forbes

    London School of Hygiene & Tropical Medicine

    Affiliation as printed

    London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK

11. Caroline Minassian

    University of Oxford

    Affiliation as printed

    The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX26GG, UK

12. Caroline E Morton

    London School of Hygiene & Tropical Medicine

    Affiliation as printed

    London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK

13. Emily Nightingale

    University of Oxford

    Affiliation as printed

    The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX26GG, UK

14. Amir Mehrkar

    University of Oxford

    Affiliation as printed

    The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX26GG, UK

15. David Evans

    University of Oxford

    Affiliation as printed

    The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX26GG, UK

16. Brian David Nicholson

    London School of Hygiene & Tropical Medicine

    Affiliation as printed

    London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK

17. David A. Leon

    University of Oxford

    Affiliation as printed

    The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX26GG, UK

18. Peter Inglesby

    University of Oxford

    Affiliation as printed

    The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX26GG, UK

19. Brian MacKenna
    Affiliation as printed

    TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, UK

20. Jonathan Cockburn

    London School of Hygiene & Tropical Medicine

    Affiliation as printed

    London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK

21. Nicholas G. M. Davies

    University of Oxford

    Affiliation as printed

    The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX26GG, UK

22. William J. Hulme

    University of Oxford

    Affiliation as printed

    The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX26GG, UK

23. Jessica Morley

    London School of Hygiene & Tropical Medicine

    Affiliation as printed

    London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK

24. Ian Douglas

    London School of Hygiene & Tropical Medicine

    Affiliation as printed

    London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK

25. Christopher T. Rentsch

    London School of Hygiene & Tropical Medicine

    Affiliation as printed

    London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK

26. Rohini Mathur

    London School of Hygiene & Tropical Medicine

    Affiliation as printed

    London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK

27. Angel Y. S. Wong

    London School of Hygiene & Tropical Medicine

    Affiliation as printed

    London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK

28. Anna Schultze

    University of Oxford

    Affiliation as printed

    The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX26GG, UK

29. Richard Croker
    Affiliation as printed

    TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, UK

30. John V. Parry
    Affiliation as printed

    TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, UK

31. Frank Hester
    Affiliation as printed

    TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, UK

32. Sam B. Harper

    University of Oxford

    Affiliation as printed

    Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK

33. Rafael Perera

    London School of Hygiene & Tropical Medicine

    Affiliation as printed

    London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK

34. Richard Grieve

    Intensive Care National Audit & Research Centre

    Affiliation as printed

    ICNARC, 24 High Holborn, Holborn, London, WC1V 6AZ, UK

35. David A Harrison Aachen

    Leiden University Medical Center

    Affiliation as printed

    Leiden University Medical Center and Erasmus MC, Leiden, The Netherlands

36. Ewout Willem Steyerberg

    London School of Hygiene & Tropical Medicine

    Affiliation as printed

    London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK

37. Rosalind M. Eggo

    London School of Hygiene & Tropical Medicine

    Affiliation as printed

    London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK

38. Karla Diaz-Ordaz

    London School of Hygiene & Tropical Medicine

    Affiliation as printed

    London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK

39. Ruth H. Keogh

    London School of Hygiene & Tropical Medicine

    Affiliation as printed

    London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK

40. Stephen Evans

    London School of Hygiene & Tropical Medicine

    Affiliation as printed

    London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK

41. Liam L Smeeth

    University of Oxford

    Affiliation as printed

    The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, OX26GG, UK

42. Ben M. Goldacre